Basically any time I play as allies, I have 2 uses for subs early game, depending on their torpedoes.
Now granted I am very rusty since I have not played a PBEM in a long time, but from my memory, these are the things I've done.
The good torpedo subs I send to the SRA where you are sure to find a lot of tankers and merchant ships, which are the most valuable targets in the long run.
The other boats with bad torpedoes are really best used to ferry troops or supplies until the torpedoes are fixed. They can move a decent amount of supplies 36-48 for most of the subs, and are not so easy to intercept, unlike your AKs would be. Meaning you might just be able to hold the places you need to hold a short bit longer. Delay for the IJN player is always bad.
And as a mostly IJN player, I can tell you this. As the Allies place your sub patrols where they do not go into shallow water. For the first year of the game, the IJN basically doesn't have any depth charges that can drop deep enough to hit your subs in deep water, meaning they can't damage your subs. The Type 95 DC simply can't go deep enough to hit a sub that dives deep in deep water. When your opponent starts getting the Type 95 Mod-2 and Type 2 depth charges that will change. I think the first ships start getting the Type 95 Mod-2 around 4/42 or so.
Once Singapore and Palembang fall, you will want to set up sub patrols in the waters north of Borneo, because big convoys will have to go through there to get back and forth between the oil/resource bases and the Home Islands. You may end up basing subs out of Darwin or Broome (just place some AS there) or even from Calcutta. One thing I would not do is put too many subs near the Home Islands, if your opponent has any experience, he will have a lot of ASW patrols and aircraft doing ASW there. Same for Takao as the waters around there are a good choke point.
Anyway, my advice may be obsolete since I haven't played a PBEM in such a long time, but I hope it helps or gives you some new ideas.
I use all my subs for one basic purpose. That is to sink ships. Putting them on other missions (other than once in a while) is a waste of assets. I do not worry about shallow water in 1942. Japanese ASW is very weak and will remain so until late 43. Their best ASW asset is to train up as many bombers as they can and that takes time. Never mind the lousy torpedoes on the fleet boats. Considering that you run only a small risk of losing a sub to Japanese ASW in 1942, go ahead and put them into combat. A lousy chance to hit is better than no chance at all which is what you have if you do not deploy them. They will have some success regardless. In 1942 a torpedo hit on the Akagi can be a balance of power changer in your next carrier battle. The S boats are useful and generally patrol near where the fighting is heaviest. But the MK-10 is a weaker torpedo. Use your AS type ships to support them. Port size does not matter much then.
I am the Holy Roman Emperor and am above grammar.
Sigismund of Luxemburg